Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2 (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme sequence database and (iii) Hotpep search against the conserved CAZyme short peptide database. Combining the three outputs and removing CAZymes found by only one tool can significantly improve the CAZome annotation accuracy. In addition, dbCAN2 now also accepts nucleotide sequence submission, and offers the service to predict physically linked CAZyme gene clusters (CGCs), which will be a very useful online tool for identifying putative polysaccharide utilization loci (PULs) in microbial genomes or metagenomes.

Carbohydrate-active enzyme (CAZymes) are not only the most important enzymes for bioenergy and agricultural industries, but also very important for human health, in that human gut microbiota encode hundreds of CAZyme genes in their genomes for degrading various dietary and host carbohydrates. We have built an online database dbCAN-seq (http://cys.bios.niu.edu/dbCAN_seq) to provide pre-computed CAZyme sequence and annotation data for 5,349 bacterial genomes. Compared to the other CAZyme resources, dbCAN-seq has the following new features: (i) a convenient download page to allow batch download of all the sequence and annotation data; (ii) an annotation page for every CAZyme to provide the most comprehensive annotation data; (iii) a metadata page to organize the bacterial genomes according to species metadata such as disease, habitat, oxygen requirement, temperature, metabolism; (iv) a very fast tool to identify physically linked CAZyme gene clusters (CGCs) and (v) a powerful search function to allow fast and efficient data query. With these unique utilities, dbCAN-seq will become a valuable web resource for CAZyme research, with a focus complementary to dbCAN (automated CAZyme annotation server) and CAZy (CAZyme family classification and reference database).

Modeling the evolution of user feedback and social links in dynamic social networks is of considerable significance, because it is the basis of many applications, including recommendation systems and user behavior analyses. Most of the existing methods in this area model user behaviors separately and consider only certain aspects of this problem, such as dynamic preferences of users, dynamic attributes of items, evolutions of social networks, and their partial integration. This work proposes a comprehensive general neural framework with several optimal strategies to jointly model the evolution of user feedback and social links. The framework considers the dynamic user preferences, dynamic item attributes, and time-dependent social links in time evolving social networks. Experimental results conducted on two real-world datasets demonstrate that our proposed model performs remarkably better than state-of-the-art methods.

Cardinality estimation is a fundamental problem in database systems. To capture the rich joint data distributions of a relational table, most of the existing work either uses data as unsupervised information or uses query workload as supervised information. Very little work has been done to use both types of information, and cannot fully make use of both types of information to learn the joint data distribution. In this work, we aim to close the gap between data-driven and query-driven methods by proposing a new unified deep autoregressive model, UAE, that learns the joint data distribution from both the data and query workload. First, to enable using the supervised query information in the deep autoregressive model, we develop differentiable progressive sampling using the Gumbel-Softmax trick. Second, UAE is able to utilize both types of information to learn the joint data distribution in a single model. Comprehensive experimental results demonstrate that UAE achieves single-digit multiplicative error at tail, better accuracies over state-of-the-art methods, and is both space and time efficient.

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